The bodies of three refugees were found in the northeast of the Greek island of Mykonos, after their boat sank on Friday morning, according to what the Greek Coast Guard announced.
According to preliminary information, the dead are two women and a man, whose nationalities the Greek authorities did not specify.
A search and rescue operation is underway to try to find the other three people who were picked up and brought to safety by two survivors who said they were traveling with them.
Two Coast Guard ships, a helicopter and land vehicles are involved in the search.
For months, migrants have been trying to cross directly from the Turkish coast to Italy, taking a new route through the Cyclades, which attract thousands of tourists every summer.
This new route, according to the NGO, aims to avoid the North Aegean islands where testimonies and videos of forced returns by Greece are on the rise.
Athens has always rejected these accusations, despite repeated testimonies from migrants and reports from NGOs.
Under European rules, the first country from which a migrant enters the EU is responsible for his or her asylum application.